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Soil fertility directly depends on soil biota (for example, the decomposition of biopolymers necessary for the formation of soil humus from which the fertility of soils largely depends). The decomposition of plant residues occurs as a result of the interaction of soil microorganisms and animals. The study of the physiological state and ecological strategies of intestinal microorganisms is important because it makes it possible to understand the mechanism of such interactions. One of the most significant representatives of soil animals for fertility is earthworms. Thus, Aporrectodea caliginosa and the sample of the humus-accumulative horizon of sod-podzolic soil were chosen for the research. The objective of the research is the study of transit bacterial populations of the intestine Aporrectodea caliginosa, comparison in soil and coprolites of biodiversity, physiological diversity and physiological state of its members. The results were obtained that the Berger-Parker indices show a decrease in domination of one species after the passage. The Berger-Parker indices of soil and coprolites were 0.72 and 0.67 respectively. The Shannon index shows that the species diversity is higher after passage. The Shannon indices of soil and coprolites were 0.96 and 1.27 respectively. In the experiment, the growth curves of bacteria on liquid media (8 polymers: pectin, casein, dextran 500, carboxymethyl cellulose (cmc), chitin, tween 20, xylan, starch) were obtained. The equation of growth in the lag phase was used to calculate the parameters the metabolic readiness of associations for growth and the maximum specific growth rate. As a result of the passage, the proportion of associations with large values of the maximum specific growth rate increases. This was an increase from 0.084 in soil to 0.091 in coprolites. This indicates an increase in r-strategists in the bacterial transit community at passage. Physiological state, i.e. the metabolic readiness of associations for growth on polymers increased with passage through the intestine. This was an increase from 0.049 in soil to 0.102 in coprolites. Thus, we can make a conclusion that the passage has a significant influence on the microbial community of the soil. Due to this process, microorganisms become more active (metabolic readiness for growth increases, specific growth rate increases). The microbial community becomes more stable (the species composition becomes more aligned and diverse).